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Hlaváč V, Červenková L, Šůsová S, Holý P, Liška V, Vyčítal O, Šorejs O, Fiala O, Daum O, Souček P. Exome Sequencing of Paired Colorectal Carcinomas and Synchronous Liver Metastases for Prognosis and Therapy Prediction. JCO Precis Oncol 2023; 7:e2200557. [PMID: 37141551 DOI: 10.1200/po.22.00557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
PURPOSE Analysis of somatic variant profiles in retrospectively collected pairs of primary tumors and synchronous liver metastases from surgically treated patients with colorectal carcinomas. Mutational profiles were compared between groups of patients stratified by response to chemotherapy and survival. PATIENTS AND METHODS The study used whole-exome sequencing of tumor sample pairs from 20 patients diagnosed and treated at a single center. The Cancer Genome Atlas COAD-READ data set (n = 380) was used for validation in silico, where possible. RESULTS The most frequently altered oncodrivers were APC (55% in primaries and 60% in metastases), TP53 (50/45), TRIP11 (30/5), FAT4 (20/25), and KRAS (15/25). Harboring variants with a high or moderate predicted functional effect in KRAS in primary tumors was significantly associated with poor relapse-free survival in both our sample set and the validation data set. We found a number of additional prognostic associations, including mutational load, alterations in individual genes, oncodriver pathways, and single base substitution (SBS) signatures in primary tissues, which were not confirmed by validation. Altered ATM, DNAH11, and MUC5AC, or a higher share of SBS24 signature in metastases seemed to represent poor prognostic factors, but because of a lack of suitable validation data sets, these results must be treated with extreme caution. No gene or profile was significantly associated with response to chemotherapy. CONCLUSION Taken together, we report subtle differences in exome mutational profiles between paired primary tumors and synchronous liver metastases and a distinct prognostic relevance of KRAS in primary tumors. Although the general scarcity of primary tumor-synchronous metastasis sample pairs with high-quality clinical data makes robust validation difficult, this study provides potentially valuable data for utilization in precision oncology and could serve as a springboard for larger studies.
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Affiliation(s)
- Viktor Hlaváč
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Lenka Červenková
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Simona Šůsová
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Petr Holý
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Václav Liška
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Vyčítal
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Surgery, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Šorejs
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Fiala
- Laboratory of Translational Cancer Genomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Oncology and Radiotherapeutics, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Ondřej Daum
- Department of Pathology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Souček
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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Standards for Quantitative Measurement of DNA Damage in Mammalian Cells. Int J Mol Sci 2023; 24:ijms24065427. [PMID: 36982502 PMCID: PMC10051712 DOI: 10.3390/ijms24065427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
As the potential applications of DNA diagnostics continue to expand, there is a need for improved methods and standards for DNA analysis. This report describes several methods that could be considered for the production of reference materials for the quantitative measurement of DNA damage in mammalian cells. With the focus on DNA strand breaks, potentially useful methods for assessing DNA damage in mammalian cells are reviewed. The advantages and limitations of each method, as well as additional concerns with respect to reference material development, are also discussed. In conclusion, we outline strategies for developing candidate DNA damage reference materials that could be adopted by research laboratories in a wide variety of applications.
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Hlavac V, Mohelnikova-Duchonova B, Lovecek M, Ehrmann J, Brynychova V, Kolarova K, Soucek P. Targeted Sequencing of Pancreatic Adenocarcinomas from Patients with Metachronous Pulmonary Metastases. Genes (Basel) 2020; 11:E1391. [PMID: 33255265 PMCID: PMC7760784 DOI: 10.3390/genes11121391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/24/2022] Open
Abstract
Mutation spectra of 250 cancer driver, druggable, and actionable genes were analyzed in surgically resected pancreatic ductal adenocarcinoma (PDAC) patients who developed metachronous pulmonary metastases. Targeted sequencing was performed in DNA from blood and archival samples of 15 primary tumors and three paired metastases. Results were complemented with the determination of G12V mutation in KRAS by droplet digital PCR. The median number of protein-changing mutations was 52 per patient. KRAS and TP53 were significantly enriched in fractions of mutations in hotspots. Individual gene mutation frequencies or mutational loads accounting separately for drivers, druggable, or clinically actionable genes, did not significantly associate with patients' survival. LRP1B was markedly mutated in primaries of patients who generalized (71%) compared to those developing solitary pulmonary metastases (0%). FLG2 was mutated exclusively in primary tumors compared to paired metastases. In conclusion, signatures of prognostically differing subgroups of PDAC patients were generated for further utilization in precision medicine.
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Affiliation(s)
- Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic; (B.M.-D.); (K.K.)
| | - Martin Lovecek
- Department of Surgery I, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic;
| | - Jiri Ehrmann
- Department of Clinical and Molecular Pathology, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic;
| | - Veronika Brynychova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
| | - Katerina Kolarova
- Department of Oncology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 779 00 Olomouc, Czech Republic; (B.M.-D.); (K.K.)
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic; (V.B.); (P.S.)
- Toxicogenomics Unit, National Institute of Public Health, 100 42 Prague, Czech Republic
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Reece M, Saluja H, Hollington P, Karapetis CS, Vatandoust S, Young GP, Symonds EL. The Use of Circulating Tumor DNA to Monitor and Predict Response to Treatment in Colorectal Cancer. Front Genet 2019; 10:1118. [PMID: 31824558 PMCID: PMC6881479 DOI: 10.3389/fgene.2019.01118] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/16/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Colorectal cancer is one of the most common cancers worldwide and has a high mortality rate following disease recurrence. Treatment efficacy is maximized by providing tailored cancer treatment, ideally involving surgical resection and personalized neoadjuvant and adjuvant therapies, including chemotherapy, radiotherapy and increasingly, targeted therapy. Early detection of recurrence or disease progression results in more treatable disease and is essential to improving survival outcomes. Recent advances in the understanding of tumor genetics have resulted in the discovery of circulating tumor DNA (ctDNA). A growing body of evidence supports the use of these sensitive biomarkers in detecting residual disease and diagnosing recurrence as well as enabling targeted and tumor-specific adjuvant therapies. Methods: A literature search in Pubmed was performed to identify all original articles preceding April 2019 that utilize ctDNA for the purpose of monitoring response to colorectal cancer treatment. Results: Ninety-two clinical studies were included. These studies demonstrate that ctDNA is a reliable measure of tumor burden. Studies show the utility of ctDNA in assessing the adequacy of surgical tumor clearance and changes in ctDNA levels reflect response to systemic treatments. ctDNA can be used in the selection of targeted treatments. The reappearance or increase in ctDNA, as well as the emergence of new mutations, correlates with disease recurrence, progression, and resistance to therapy, with ctDNA measurement allowing more sensitive monitoring than currently used clinical tools. Conclusions: ctDNA shows enormous promise as a sensitive biomarker for monitoring response to many treatment modalities and for targeting therapy. Thus, it is emerging as a new way for guiding treatment decisions-initiating, altering, and ceasing treatments, or prompting investigation into the potential for residual disease. However, many potentially useful ctDNA markers are available and more work is needed to determine which are best suited for specific purposes and for improving specific outcomes.
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Affiliation(s)
- Mifanwy Reece
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Hariti Saluja
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Paul Hollington
- Colorectal Surgery, Division of Surgery & Perioperative Medicine, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Christos S Karapetis
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Sina Vatandoust
- Department of Medical Oncology, Flinders Medical Centre, Bedford Park, SA, Australia
| | - Graeme P Young
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Erin L Symonds
- Flinders Centre for Innovation in Cancer, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, SA, Australia
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